def __init__(self, hdp, tx_ac, alt_ac, alt_aln_method):
self.hdp = hdp
self.tx_ac = tx_ac
self.alt_ac = alt_ac
self.alt_aln_method = alt_aln_method
if self.alt_aln_method != 'transcript':
self.tx_info = hdp.get_tx_info(self.tx_ac, self.alt_ac, self.alt_aln_method)
if self.tx_info is None:
raise HGVSError("TranscriptMapper(tx_ac={self.tx_ac}, "
"alt_ac={self.alt_ac}, alt_aln_method={self.alt_aln_method}): "
"No transcript info".format(self=self))
self.tx_exons = hdp.get_tx_exons(self.tx_ac, self.alt_ac, self.alt_aln_method)
if self.tx_info is None:
raise HGVSError("TranscriptMapper(tx_ac={self.tx_ac}, "
"alt_ac={self.alt_ac}, alt_aln_method={self.alt_aln_method}): "
"No transcript exons".format(self=self))
self.strand = self.tx_exons[0]['alt_strand']
self.cds_start_i = self.tx_info['cds_start_i']
self.cds_end_i = self.tx_info['cds_end_i']
self.gc_offset = self.tx_exons[0]['alt_start_i']
self.cigar = build_tx_cigar(self.tx_exons, self.strand)
self.im = hgvs.intervalmapper.IntervalMapper.from_cigar(self.cigar)
self.tgt_len = self.im.tgt_len
else:
# this covers the identity cases r <-> c
self.tx_identity_info = hdp.get_tx_identity_info(self.tx_ac)
self.cds_start_i = self.tx_identity_info['cds_start_i']
self.cds_end_i = self.tx_identity_info['cds_end_i']
self.tgt_len = sum(self.tx_identity_info['lengths'])
def __init__(self, hdp, tx_ac, alt_ac, alt_aln_method):
self.tx_ac = tx_ac
self.alt_ac = alt_ac
self.alt_aln_method = alt_aln_method
if self.alt_aln_method != "transcript":
tx_info = hdp.get_tx_info(self.tx_ac, self.alt_ac,
self.alt_aln_method)
if tx_info is None:
raise HGVSDataNotAvailableError(
"AlignmentMapper(tx_ac={self.tx_ac}, "
"alt_ac={self.alt_ac}, alt_aln_method={self.alt_aln_method}): "
"No transcript info".format(self=self))
tx_exons = hdp.get_tx_exons(self.tx_ac, self.alt_ac,
self.alt_aln_method)
if tx_exons is None:
raise HGVSDataNotAvailableError(
"AlignmentMapper(tx_ac={self.tx_ac}, "
"alt_ac={self.alt_ac}, alt_aln_method={self.alt_aln_method}): "
"No transcript exons".format(self=self))
# hgvs-386: An assumption when building the cigar string
# is that exons are adjacent. Assert that here.
sorted_tx_exons = sorted(tx_exons, key=lambda e: e["ord"])
for i in range(1, len(sorted_tx_exons)):
if sorted_tx_exons[
i - 1]["tx_end_i"] != sorted_tx_exons[i]["tx_start_i"]:
raise HGVSDataNotAvailableError(
"AlignmentMapper(tx_ac={self.tx_ac}, "
"alt_ac={self.alt_ac}, alt_aln_method={self.alt_aln_method}): "
"Exons {a} and {b} are not adjacent".format(self=self,
a=i,
b=i + 1))
self.strand = tx_exons[0]["alt_strand"]
self.gc_offset = tx_exons[0]["alt_start_i"]
self.cds_start_i = tx_info["cds_start_i"]
self.cds_end_i = tx_info["cds_end_i"]
self.cigar = build_tx_cigar(tx_exons, self.strand)
self.ref_pos, self.tgt_pos, self.cigar_op = self._parse_cigar(
self.cigar)
self.tgt_len = self.tgt_pos[-1]
else:
# this covers the identity cases n <-> c
tx_identity_info = hdp.get_tx_identity_info(self.tx_ac)
if tx_identity_info is None:
raise HGVSDataNotAvailableError(
"AlignmentMapper(tx_ac={self.tx_ac}, "
"alt_ac={self.alt_ac}, alt_aln_method={self.alt_aln_method}): "
"No transcript identity info".format(self=self))
self.cds_start_i = tx_identity_info["cds_start_i"]
self.cds_end_i = tx_identity_info["cds_end_i"]
self.tgt_len = sum(tx_identity_info["lengths"])
assert not (
(self.cds_start_i is None) ^ (self.cds_end_i is None)
), "CDS start and end must both be defined or neither defined"